Lester Hedges

Thanks, @jmichel80. I should be able to take a look later today.

Here's a minimal example of the issue using BioSimSpace: Sire < 2023: ```python import BioSimSpace as BSS from Sire.Mol import AtomIdx, Selector_Atom_ # Load an example system and get the...

Sorry, it works on < 2023. Apologies if that wasn't clear in the example, or if I made a typo. In my first example, it works if the selector is...

Okay, I've made some modifications to SOMD and it now _appears_ to be working. (It starts up and runs without crashing, at least.) Could you check this at your end...

I've now added a basic SOMD FEP test to BioSimSpace on my current feature branch [here](https://github.com/michellab/BioSimSpace/commit/904a25283a9d9262f8c7cfe0cf287c97f921e011). This fails with the current Sire 2023, but passes with the application of the...

I also discovered an issue with the `generateDistanceRestraintsDict` function which was (incorrectly) assuming that the solute would be `MolNum(1)`. I've switched this to using the `getSolute` function, which will be...

No problem. My edits are now available in [this](https://github.com/michellab/Sire/tree/fix-somd-2023) fix branch. @jmichel80: Let me know when you're happy and I'll create a PR against devel. Cheers.

It is also possible to work around the issue by calling `.selection()` on the solute, then calling `.selectNone()`, the using `.select()` to add the atoms of interest. For example: ```python...

I've updated the legacy SireUnitTests to use `sire.legacy` from the 2023 API [here](https://github.com/michellab/SireUnitTests/tree/feature-2023). These all still pass, which is good news :+1:

Actually, it turns out that the _only_ test of SOMD (OpenMMMD.py) in the suite was [removed](https://github.com/michellab/SireUnitTests/commit/6321f2b5ded0e0741bf7d2d0fa45aab019a99203) due to difficulty porting to the new API. The commit comment even implies that...